[Swift-commit] r5931 - in SwiftApps/CMTS/scaling: . conf

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-09-18 14:30:14 -0500 (Tue, 18 Sep 2012)
New Revision: 5931

Added:
   SwiftApps/CMTS/scaling/namd_wrapper.sh
Modified:
   SwiftApps/CMTS/scaling/conf/grotthuss.cf
   SwiftApps/CMTS/scaling/conf/grotthuss.xml
   SwiftApps/CMTS/scaling/scaling.swift
Log:
namd wrapper


Modified: SwiftApps/CMTS/scaling/conf/grotthuss.cf
===================================================================
--- SwiftApps/CMTS/scaling/conf/grotthuss.cf	2012-09-18 16:10:38 UTC (rev 5930)
+++ SwiftApps/CMTS/scaling/conf/grotthuss.cf	2012-09-18 19:30:14 UTC (rev 5931)
@@ -7,5 +7,4 @@
 provider.staging.pin.swiftfiles=false
 use.wrapper.staging=false
 
-#app rmsd=$PWD/../rmsd.sh
-#app plot_pd=$PWD/../plot_pd.pl
+#app namd_wrapper=$PWD/../namd_wrapper.sh

Modified: SwiftApps/CMTS/scaling/conf/grotthuss.xml
===================================================================
--- SwiftApps/CMTS/scaling/conf/grotthuss.xml	2012-09-18 16:10:38 UTC (rev 5930)
+++ SwiftApps/CMTS/scaling/conf/grotthuss.xml	2012-09-18 19:30:14 UTC (rev 5931)
@@ -7,7 +7,7 @@
   <profile key="jobsPerNode" namespace="globus">8</profile>
   <profile key="slots" namespace="globus">1</profile>
   <profile key="maxNodes" namespace="globus">1</profile>
-  <profile key="queue" namespace="globus">devel</profile>
+  <profile key="queue" namespace="globus">compute</profile>
   <profile key="jobThrottle" namespace="karajan">5.99</profile>
   <profile key="initialScore" namespace="karajan">10000</profile>
   <profile key="count" namespace="globus">1</profile>

Added: SwiftApps/CMTS/scaling/namd_wrapper.sh
===================================================================
--- SwiftApps/CMTS/scaling/namd_wrapper.sh	                        (rev 0)
+++ SwiftApps/CMTS/scaling/namd_wrapper.sh	2012-09-18 19:30:14 UTC (rev 5931)
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+echo Args are: $@
+echo Node file is: $PBS_NODEFILE
+echo Contents of nodefile: $( cat $PBS_NODEFILE )
+
+sed -ei 's/_WORK_/$PWD/g' h0_eq.conf
+
+mpiexec namd2 h0_eq.conf
+


Property changes on: SwiftApps/CMTS/scaling/namd_wrapper.sh
___________________________________________________________________
Added: svn:executable
   + *

Modified: SwiftApps/CMTS/scaling/scaling.swift
===================================================================
--- SwiftApps/CMTS/scaling/scaling.swift	2012-09-18 16:10:38 UTC (rev 5930)
+++ SwiftApps/CMTS/scaling/scaling.swift	2012-09-18 19:30:14 UTC (rev 5931)
@@ -20,8 +20,8 @@
 file system_restart <"h0_eq.0.restart.xsc">;
 
 foreach nodes in [minNodes:maxNodes:delta] {
-   file output <single_file_mapper; file=@strcat("logs/scaling-", nodes, ".out.txt")>;
-   file error <single_file_mapper; file=@strcat("logs/scaling-", nodes, ".err.txt")>;
+   file output <single_file_mapper; file=@strcat("logs/h0scale.", nodes, ".out")>;
+   file error <single_file_mapper; file=@strcat("logs/h0scale.", nodes, ".err")>;
    (output, error) = namd_wrapper(nodes, psf, pdb, coord_restart, velocity_restart, system_restart);
 }